代谢工程

代谢工程,也称途径工程,是基因工程一个重要分支,一般是多基因的基因工程,与细胞的基因调控、代谢调控和生化工程密切相关。讨论了代谢工程的应用,包括通过改变代谢流和代谢途径提高产量,改善生产过程,构建新的代谢途径和产生新的代谢产物等。     

代谢工程在D-核糖生产中研究现状及应用前景

简要介绍了代谢工程的进展情况,并较为详细地从宿主的选择、加速限速反应、改变代谢流和生产过程的优化等方面论述了代谢工程在D-核糖基因工程菌构建方面的应用及其应用前景。     

代谢工程及其在产苯丙氨酸基因工程菌构建中的应用

本文对代谢工程的发展状况从研究方法,在医药、农业及环保中应用等几方面做了概括地介绍;从宿主的选择,加速限速反应,改变代谢流和生产程序的优化几方面较为详细地评述了代谢工程在苯丙氨酸基因工程菌构建方面的应用,并对代谢工程的未来发展进行了展望。     

代谢工程与重组大肠杆菌的发酵

利用代谢工程可以在重组大肠杆菌的改良中减少代谢副产物乙酸的累积,优化代谢系统,利于重组蛋白质的高表达以及重组菌的高密度发酵。应用代谢工程改良重组大肠杆菌主要包括阻断乙酸产生的主要途径、限制糖酵解途径上的碳代谢流、将过量的丙酮酸转化为其它低毒的副产物以及对碳代谢流进行分流等几个方面的工作。     

代谢工程及其在产苯丙氨酸基因工程菌构建中的应用

本文对代谢工程的发展状况从研究方法,在医药物的,农业及环保中应用等几方面做了概括地介绍;从宿主的选择,加速限速反应,改变代谢流和生产程序的优化几方面较为详细地评述了代谢工程在苯丙氨酸基因工程菌构建方面的应用,并对代谢工程的未来发展进行了展望。     

代谢网络刚性与代谢工程

本文介绍了有关代谢网络,网络刚性和代谢工程的基本观点,特别是关于网络刚性和载流途径的工作假设,还讨论了代谢工程的应用与面临的难题。     

生物过程代谢组学与代谢流测定

整合的代谢组学和13C代谢流数据能充分反映细胞的代谢状态,对代谢组学和代谢流的测定技术已成为工业生物过程研究的重要手段,并能为工业生物过程优化和高产菌株理性设计提供重要帮助。阐述了代谢组学和代谢流测定的完整流程,包括实验方法、数据处理方法和软件工具,并综述了其在代谢途径鉴定、代谢机制解析和代谢工程等领域的应用进展。     

代谢网络刚性与代谢工程

本文介绍了有关代谢网络，网络刚性和代谢工程的基本观点，特别是关于网络刚性和载流途径的工作建设，还讨论了代谢工程的应用与面临的难题。     

从碳代谢流角度新解代谢工程策略

代谢工程通过改造微生物代谢过程,进而利用微生物生产各种有用的医药、化学产品及工业原料.本文从细胞代谢中碳代谢流的角度入手,将代谢工程的传统与新型策略进行分类解析.其中,传统代谢工程手段主要对目标代谢路径的关键酶进行改造,通过过表达或基因敲除增大目的代谢路径碳代谢流.然而,在代谢路径改造需要进行多基因表达的情况下,传统手段在如何最佳表达多种酶使碳流通畅上会受到很大限制.本文提出利用高碳流路径,通过简单基因改造以获得高效目标产物生产的新策略.同时,随着合成生物学与系统生物学的发展,精细调控多基因表达成为可能.本文进一步举例讨论了代谢工程中粗略与精细调控基因表达水平对碳流的影响,以期对教学与前沿科研有助.     

苯丙氨酸生物合成的研究进展

代谢工程是利用分子生物学原理系统分析代谢途径,设计合理的遗传修饰策略从而优化细胞的生物学特性,本对代谢工程及其在氨基酸生产上的应用进行了简单的回顾,比较了苯丙氨酸的几种合成途径,重点综述了苯丙氨酸生物合成的代谢途径,相关酶及其调控方式,代谢流和转运系统的分析研究,并对苯丙氨酸生产策略的优化及未来发展进行了展望。     

Physiologically Shrinking the Solution Space of a Saccharomyces cerevisiae Genome-Scale Model Suggests the Role of the Metabolic Network in Shaping Gene Expression Noise

Sampling the solution space of genome-scale models is generally conducted to determine the feasible region for metabolic flux distribution. Because the region for actual metabolic states resides only in a small fraction of the entire space, it is necessary to shrink the solution space to improve the predictive power of a model. A common strategy is to constrain models by integrating extra datasets such as high-throughput datasets and C¹³-labeled flux datasets. However, studies refining these approaches by performing a meta-analysis of massive experimental metabolic flux measurements, which are closely linked to cellular phenotypes, are limited. In the present study, experimentally identified metabolic flux data from 96 published reports were systematically reviewed. Several strong associations among metabolic flux phenotypes were observed. These phenotype-phenotype associations at the flux level were quantified and integrated into a Saccharomyces cerevisiae genome-scale model as extra physiological constraints. By sampling the shrunken solution space of the model, the metabolic flux fluctuation level, which is an intrinsic trait of metabolic reactions determined by the network, was estimated and utilized to explore its relationship to gene expression noise. Although no correlation was observed in all enzyme-coding genes, a relationship between metabolic flux fluctuation and expression noise of genes associated with enzyme-dosage sensitive reactions was detected, suggesting that the metabolic network plays a role in shaping gene expression noise. Such correlation was mainly attributed to the genes corresponding to non-essential reactions, rather than essential ones. This was at least partially, due to regulations underlying the flux phenotype-phenotype associations. Altogether, this study proposes a new approach in shrinking the solution space of a genome-scale model, of which sampling provides new insights into gene expression noise.     

Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method

A new algorithm was developed for the estimation of the metabolic flux distribution based on GC-MS data of proteinogenic amino acids. By using a sensitive GC-MS protocol as well as by combining the global search algorithm such as the genetic algorithm with the local search algorithm such as the Levenberg-Marquardt algorithm, not only the distribution of the net fluxes in the entire network, but also certain exchange fluxes which contribute significantly to the isotopomer distribution could be quantified. This mass isotopomer analysis could identify the biochemical changes involved in the regulation where acetate or glucose was used as a main carbon source. The metabolic flux analysis clearly revealed that when the specific growth rate increased, only a slight change in flux distribution was observed for acetate metabolism, indicating that subtle regulation mechanism exists in certain key junctions of this network system. Different from acetate metabolism, when glucose was used as a carbon source, as the growth rate increased, a significant increase in relative pentose phosphate pathway (PPP) flux was observed for Escherichia coli K12 at the expense of the citric acid cycle, suggesting that when growing on glucose, the flux catalyzed by isocitrate dehydrogenase could not fully fulfill the NADPH demand for cell growth, causing the oxidative PPP to be utilized to a larger extent so as to complement the NADPH demand. The GC-MS protocol as well as the new algorithm demonstrated here proved to be a powerful tool for characterizing metabolic regulation and can be utilized for strain improvement and bioprocess optimization.     

Effect of ethanol, acetate, and phenol on toluene degradation activity and tod-lux expression in Pseudomonas putida TOD102: evaluation of the metabolic flux dilution model

The reporter strain Pseudomonas putida TOD102 (with a tod-lux fusion) was used in chemostat experiments with binary substrate mixtures to investigate the effect of potentially occurring cosubstrates on toluene degradation activity. Although toluene was simultaneously utilized with other cosubstrates, its metabolic flux (defined as the toluene utilization rate per cell) decreased with increasing influent concentrations of ethanol, acetate, or phenol. Three inhibitory mechanisms were considered to explain these trends: (1) repression of the tod gene (coding for toluene dioxygenase) by acetate and ethanol, which was quantified by a decrease in specific bioluminescence; (2) competitive inhibition of toluene dioxygenase by phenol; and (3) metabolic flux dilution (MFD) by all three cosubstrates. Based on experimental observations, MFD was modeled without any fitting parameters by assuming that the metabolic flux of a substrate in a mixture is proportional to its relative availability (expressed as a fraction of the influent total organic carbon). Thus, increasing concentrations of alternative carbon sources "dilute" the metabolic flux of toluene without necessarily repressing tod, as observed with phenol (a known tod inducer). For all cosubstrates, the MFD model slightly overpredicted the measured toluene metabolic flux. Incorporating catabolite repression (for experiments with acetate or ethanol) or competitive inhibition (for experiments with phenol) with independently obtained parameters resulted in more accurate fits of the observed decrease in toluene metabolic flux with increasing cosubstrate concentration. These results imply that alternative carbon sources (including inducers) are likely to hinder toluene utilization per unit cell, and that these effects can be accurately predicted with simple mathematical models.     

Shewanella oneidensis MR-1 fluxome under various oxygen conditions

The central metabolic fluxes of Shewanella oneidensis MR-1 were examined under carbon-limited (aerobic) and oxygen-limited (microaerobic) chemostat conditions, using 13C-labeled lactate as the sole carbon source. The carbon labeling patterns of key amino acids in biomass were probed using both gas chromatography-mass spectrometry (GC-MS) and 13C nuclear magnetic resonance (NMR). Based on the genome annotation, a metabolic pathway model was constructed to quantify the central metabolic flux distributions. The model showed that the tricarboxylic acid (TCA) cycle is the major carbon metabolism route under both conditions. The Entner-Doudoroff and pentose phosphate pathways were utilized primarily for biomass synthesis (with a flux below 5% of the lactate uptake rate). The anaplerotic reactions (pyruvate to malate and oxaloacetate to phosphoenolpyruvate) and the glyoxylate shunt were active. Under carbon-limited conditions, a substantial amount (9% of the lactate uptake rate) of carbon entered the highly reversible serine metabolic pathway. Under microaerobic conditions, fluxes through the TCA cycle decreased and acetate production increased compared to what was found for carbon-limited conditions, and the flux from glyoxylate to glycine (serine-glyoxylate aminotransferase) became measurable. Although the flux distributions under aerobic, microaerobic, and shake flask culture conditions were different, the relative flux ratios for some central metabolic reactions did not differ significantly (in particular, between the shake flask and aerobic-chemostat groups). Hence, the central metabolism of S. oneidensis appears to be robust to environmental changes. Our study also demonstrates the merit of coupling GC-MS with 13C NMR for metabolic flux analysis to reduce the use of 13C-labeled substrates and to obtain more-accurate flux values.     

Dynamic flux balance analysis of the metabolism of Saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis

Dynamic flux balance analysis was utilized to simulate the metabolic behaviour of initially fully respirative and respirofermentative steady-state cultures of Saccharomyces?cerevisiae during sudden oxygen depletion. The hybrid model for the dynamic flux balance analysis included a stoichiometric genome-scale metabolic model as a static part and dynamic equations for the uptake of glucose and the cessation of respirative metabolism. The yeast consensus genome-scale metabolic model [Herrg?rd MJ et?al. (2008) Nat Biotechnol26, 1155-1160; Dobson PD et?al. (2010) BMC Syst Biol4, 145] was refined with respect to oxygen-dependent energy metabolism and further modified to reflect S.?cerevisiae anabolism in the absence of oxygen. Dynamic flux balance analysis captured well the essential features of the dynamic metabolic behaviour of S.?cerevisiae during adaptation to anaerobiosis. Modelling and simulation enabled the identification of short time-scale flux distribution dynamics under the transition to anaerobic metabolism, during which the specific growth rate was reduced, as well as longer time-scale process dynamics when the specific growth rate recovered. Expression of the metabolic genes was set into the context of the identified dynamics. Metabolic gene expression responses associated with the specific growth rate and with the cessation of respirative metabolism were distinguished.     

碳源对琥珀酸放线杆菌发酵产丁二酸的影响及其代谢流量分析

在厌氧条件下, Actinobacillus succinogenes能够利用单糖、双糖和糖醇等碳水化合物发酵生成丁二酸, 其中以山梨醇为碳源时丁二酸的产量最高。代谢流量分析结果表明: 与葡萄糖发酵相比较, 由于代谢系统中积累了更多的NADH, 使得代谢网络关键节点PYR和AcCoA处的代谢流量分配有了较大的变化, 导致更多的碳源流向丁二酸和乙醇, 而乙酸和甲酸的分泌相对减少。     

Shewanella oneidensis MR-1 Fluxome under Various Oxygen Conditions

The central metabolic fluxes of Shewanella oneidensis MR-1 were examined under carbon-limited (aerobic) and oxygen-limited (microaerobic) chemostat conditions, using ¹³C-labeled lactate as the sole carbon source. The carbon labeling patterns of key amino acids in biomass were probed using both gas chromatography-mass spectrometry (GC-MS) and ¹³C nuclear magnetic resonance (NMR). Based on the genome annotation, a metabolic pathway model was constructed to quantify the central metabolic flux distributions. The model showed that the tricarboxylic acid (TCA) cycle is the major carbon metabolism route under both conditions. The Entner-Doudoroff and pentose phosphate pathways were utilized primarily for biomass synthesis (with a flux below 5% of the lactate uptake rate). The anaplerotic reactions (pyruvate to malate and oxaloacetate to phosphoenolpyruvate) and the glyoxylate shunt were active. Under carbon-limited conditions, a substantial amount (9% of the lactate uptake rate) of carbon entered the highly reversible serine metabolic pathway. Under microaerobic conditions, fluxes through the TCA cycle decreased and acetate production increased compared to what was found for carbon-limited conditions, and the flux from glyoxylate to glycine (serine-glyoxylate aminotransferase) became measurable. Although the flux distributions under aerobic, microaerobic, and shake flask culture conditions were different, the relative flux ratios for some central metabolic reactions did not differ significantly (in particular, between the shake flask and aerobic-chemostat groups). Hence, the central metabolism of S. oneidensis appears to be robust to environmental changes. Our study also demonstrates the merit of coupling GC-MS with ¹³C NMR for metabolic flux analysis to reduce the use of ¹³C-labeled substrates and to obtain more-accurate flux values.     

Investigation of the anaerobic metabolism of Rhodobacter capsulatus with a flux model

A flux model of the anaerobic metabolism of Rhodobacter capsulatus related to hydrogen production has been constructed. The performance of this model has been assessed by comparing the computed metabolic fluxes with experimental values obtained by several research groups who worked on various strains of R. capsulatus and utilized different growth setups. We have investigated the photoheterotrophic metabolism of R. capsulatus on acetate and have shown that in this mode the bacterium can produce hydrogen or biopolymers. Analysis of the flux model reveled several mutants that can evolve hydrogen with a higher rate than the wild type.     

Carbon flux through tricarboxylic acid cycle in rat renal tubules

Our aim was to delineate the effect(s) of chronic metabolic acidosis on renal TCA-cycle metabolism. Renal tubules isolated from control and chronically acidotic rats were incubated at pH 7.4 with either 2 mM [2,3-13C]pyruvate or [2-13C]acetate. GC-MS and/or 13C-NMR were utilized to monitor the flux of 13C through pyruvate dehydrogenase, pyruvate carboxylase and the TCA-cycle. With either, precursor acidosis was associated with significantly decreased formation of 13C-labelled citrate, malate, aspartate and alanine and increased formation of glucose, lactate and acetyl-CoA as compared with the control. The results indicate that adaptation of renal metabolism to chronic metabolic acidosis is associated with diminished flux through citrate synthetase and concomitantly increased flux through pyruvate carboxylase. The data suggest that depletion of TCA-cycle intermediates and enhanced ammoniagenesis in the kidney of chronically acidotic rats may be regulated at the site of mitochondrial citrate-condensing enzyme.